src/visitors/AtomVisitor.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include <cstring>
#include "visitors/AtomVisitor.hpp"
#include "primitives/DirectionalAtom.hpp"
#include "primitives/RigidBody.hpp"
#include "types/MultipoleAdapter.hpp"
#include "types/GayBerneAdapter.hpp"

namespace OpenMD {
  void BaseAtomVisitor::visit(RigidBody *rb) {
    //vector<Atom*> myAtoms;
    //vector<Atom*>::iterator atomIter;

    //myAtoms = rb->getAtoms();

    //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
    //  (*atomIter)->accept(this);
  }

  void BaseAtomVisitor::setVisited(Atom *atom) {
    GenericData *data;
    data = atom->getPropertyByName("VISITED");

    //if visited property is not existed, add it as new property
    if (data == NULL) {
      data = new GenericData();
      data->setID("VISITED");
      atom->addProperty(data);
    }
  }

  bool BaseAtomVisitor::isVisited(Atom *atom) {
    GenericData *data;
    data = atom->getPropertyByName("VISITED");
    return data == NULL ? false : true;
  }

  //------------------------------------------------------------------------//
        
  void DefaultAtomVisitor::visit(Atom *atom) {
    AtomData *atomData;
    AtomInfo *atomInfo;
    Vector3d  pos;
    Vector3d  vel;
    Vector3d  frc;
    Vector3d  u;

    if (isVisited(atom))
      return;
    
    atomInfo = new AtomInfo;
    
    atomData = new AtomData;
    atomData->setID("ATOMDATA");
    
    pos = atom->getPos();
    vel = atom->getVel();
    frc = atom->getFrc();
    atomInfo->atomTypeName = atom->getType();
    atomInfo->pos[0] = pos[0];
    atomInfo->pos[1] = pos[1];
    atomInfo->pos[2] = pos[2];
    atomInfo->vel[0] = vel[0];
    atomInfo->vel[1] = vel[1];
    atomInfo->vel[2] = vel[2];
    atomInfo->hasVelocity = true;
    atomInfo->frc[0] = frc[0];
    atomInfo->frc[1] = frc[1];
    atomInfo->frc[2] = frc[2];
    atomInfo->hasForce = true;
    atomInfo->vec[0] = 0.0;
    atomInfo->vec[1] = 0.0;
    atomInfo->vec[2] = 0.0;
    
    atomData->addAtomInfo(atomInfo);
    
    atom->addProperty(atomData);
    
    setVisited(atom);
  }
  
  void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
    AtomData *atomData;
    AtomInfo *atomInfo;
    Vector3d  pos;
    Vector3d  vel;
    Vector3d  frc;
    Vector3d  u;

    if (isVisited(datom))
      return;
    
    pos = datom->getPos();
    vel = datom->getVel();
    frc = datom->getFrc();

    GayBerneAdapter gba = GayBerneAdapter(datom->getAtomType());
    MultipoleAdapter ma = MultipoleAdapter(datom->getAtomType());
    
    if (gba.isGayBerne()) {
      u = datom->getA().transpose()*V3Z;         
    } else if (ma.isDipole()) {
      u = datom->getDipole();
    } else if (ma.isQuadrupole()) {
      //u = datom->getQuadrupole().getColumn(2);
      u = datom->getA().transpose()*V3Z;
    }
    atomData = new AtomData;
    atomData->setID("ATOMDATA");
    atomInfo = new AtomInfo;

    atomInfo->atomTypeName = datom->getType();
    atomInfo->pos[0] = pos[0];
    atomInfo->pos[1] = pos[1];
    atomInfo->pos[2] = pos[2];
    atomInfo->vel[0] = vel[0];
    atomInfo->vel[1] = vel[1];
    atomInfo->vel[2] = vel[2];
    atomInfo->hasVelocity = true;
    atomInfo->frc[0] = frc[0];
    atomInfo->frc[1] = frc[1];
    atomInfo->frc[2] = frc[2];
    atomInfo->hasForce = true;
    atomInfo->vec[0] = u[0];
    atomInfo->vec[1] = u[1];
    atomInfo->vec[2] = u[2];
    atomInfo->hasVector = true;

    atomData->addAtomInfo(atomInfo);

    datom->addProperty(atomData);

    setVisited(datom);
  }

  const std::string DefaultAtomVisitor::toString() {
    char   buffer[65535];
    std::string result;

    sprintf(buffer,
            "------------------------------------------------------------------\n");
    result += buffer;

    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
    result += buffer;

    sprintf(buffer,
            "Visitor Description: copy atom infomation into atom data\n");
    result += buffer;

    sprintf(buffer,
            "------------------------------------------------------------------\n");
    result += buffer;

    return result;
  }
} //namespace OpenMD
Revision:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 2 months ago) by gezelter
File size:	6247 byte(s)
Log Message:	Fixed a widespread typo in the license
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	gezelter	2	#include <cstring>
44	tim	3	#include "visitors/AtomVisitor.hpp"
45			#include "primitives/DirectionalAtom.hpp"
46			#include "primitives/RigidBody.hpp"
47	gezelter	1787	#include "types/MultipoleAdapter.hpp"
48			#include "types/GayBerneAdapter.hpp"
49	gezelter	2
50	gezelter	1390	namespace OpenMD {
51	gezelter	507	void BaseAtomVisitor::visit(RigidBody *rb) {
52			//vector<Atom*> myAtoms;
53			//vector<Atom*>::iterator atomIter;
54	tim	132
55	gezelter	507	//myAtoms = rb->getAtoms();
56	gezelter	2
57	gezelter	507	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
58			// (*atomIter)->accept(this);
59			}
60	gezelter	2
61	gezelter	507	void BaseAtomVisitor::setVisited(Atom *atom) {
62	gezelter	246	GenericData *data;
63			data = atom->getPropertyByName("VISITED");
64	gezelter	2
65	gezelter	246	//if visited property is not existed, add it as new property
66			if (data == NULL) {
67	gezelter	507	data = new GenericData();
68			data->setID("VISITED");
69			atom->addProperty(data);
70	gezelter	246	}
71	gezelter	507	}
72	gezelter	2
73	gezelter	507	bool BaseAtomVisitor::isVisited(Atom *atom) {
74	gezelter	246	GenericData *data;
75			data = atom->getPropertyByName("VISITED");
76			return data == NULL ? false : true;
77	gezelter	507	}
78	gezelter	2
79	gezelter	1455	//------------------------------------------------------------------------//
80
81	gezelter	507	void DefaultAtomVisitor::visit(Atom *atom) {
82	gezelter	246	AtomData *atomData;
83			AtomInfo *atomInfo;
84			Vector3d pos;
85	gezelter	1456	Vector3d vel;
86			Vector3d frc;
87			Vector3d u;
88
89	gezelter	246	if (isVisited(atom))
90	gezelter	507	return;
91	gezelter	1455
92	gezelter	246	atomInfo = new AtomInfo;
93	gezelter	1455
94	gezelter	246	atomData = new AtomData;
95			atomData->setID("ATOMDATA");
96	gezelter	1455
97	gezelter	246	pos = atom->getPos();
98	gezelter	1456	vel = atom->getVel();
99			frc = atom->getFrc();
100	gezelter	407	atomInfo->atomTypeName = atom->getType();
101	gezelter	246	atomInfo->pos[0] = pos[0];
102			atomInfo->pos[1] = pos[1];
103			atomInfo->pos[2] = pos[2];
104	gezelter	1456	atomInfo->vel[0] = vel[0];
105			atomInfo->vel[1] = vel[1];
106			atomInfo->vel[2] = vel[2];
107			atomInfo->hasVelocity = true;
108			atomInfo->frc[0] = frc[0];
109			atomInfo->frc[1] = frc[1];
110			atomInfo->frc[2] = frc[2];
111			atomInfo->hasForce = true;
112			atomInfo->vec[0] = 0.0;
113			atomInfo->vec[1] = 0.0;
114			atomInfo->vec[2] = 0.0;
115	gezelter	1455
116	gezelter	246	atomData->addAtomInfo(atomInfo);
117	gezelter	1455
118	gezelter	246	atom->addProperty(atomData);
119	gezelter	1455
120	gezelter	246	setVisited(atom);
121	gezelter	507	}
122	gezelter	1455
123	gezelter	507	void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
124	gezelter	246	AtomData *atomData;
125			AtomInfo *atomInfo;
126			Vector3d pos;
127	gezelter	1456	Vector3d vel;
128			Vector3d frc;
129	gezelter	246	Vector3d u;
130	gezelter	2
131	gezelter	246	if (isVisited(datom))
132	gezelter	507	return;
133	gezelter	1456
134	gezelter	246	pos = datom->getPos();
135	gezelter	1456	vel = datom->getVel();
136			frc = datom->getFrc();
137	gezelter	1787
138			GayBerneAdapter gba = GayBerneAdapter(datom->getAtomType());
139			MultipoleAdapter ma = MultipoleAdapter(datom->getAtomType());
140
141			if (gba.isGayBerne()) {
142			u = datom->getA().transpose()*V3Z;
143			} else if (ma.isDipole()) {
144			u = datom->getDipole();
145	gezelter	1814	} else if (ma.isQuadrupole()) {
146	gezelter	1821	//u = datom->getQuadrupole().getColumn(2);
147			u = datom->getA().transpose()*V3Z;
148	tim	989	}
149	gezelter	246	atomData = new AtomData;
150			atomData->setID("ATOMDATA");
151			atomInfo = new AtomInfo;
152	gezelter	2
153	gezelter	407	atomInfo->atomTypeName = datom->getType();
154	gezelter	246	atomInfo->pos[0] = pos[0];
155			atomInfo->pos[1] = pos[1];
156			atomInfo->pos[2] = pos[2];
157	gezelter	1456	atomInfo->vel[0] = vel[0];
158			atomInfo->vel[1] = vel[1];
159			atomInfo->vel[2] = vel[2];
160			atomInfo->hasVelocity = true;
161			atomInfo->frc[0] = frc[0];
162			atomInfo->frc[1] = frc[1];
163			atomInfo->frc[2] = frc[2];
164			atomInfo->hasForce = true;
165			atomInfo->vec[0] = u[0];
166			atomInfo->vec[1] = u[1];
167			atomInfo->vec[2] = u[2];
168			atomInfo->hasVector = true;
169	gezelter	246
170			atomData->addAtomInfo(atomInfo);
171
172			datom->addProperty(atomData);
173
174			setVisited(datom);
175	gezelter	507	}
176	gezelter	2
177	gezelter	507	const std::string DefaultAtomVisitor::toString() {
178	gezelter	246	char buffer[65535];
179			std::string result;
180	gezelter	2
181	gezelter	246	sprintf(buffer,
182			"------------------------------------------------------------------\n");
183			result += buffer;
184	gezelter	2
185	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
186			result += buffer;
187	gezelter	2
188	gezelter	246	sprintf(buffer,
189			"Visitor Description: copy atom infomation into atom data\n");
190			result += buffer;
191	gezelter	2
192	gezelter	246	sprintf(buffer,
193			"------------------------------------------------------------------\n");
194			result += buffer;
195	gezelter	2
196	gezelter	246	return result;
197	gezelter	507	}
198	gezelter	1390	} //namespace OpenMD